Fourtime travelers from the past–Link, Gwonam, Morshu, and King Harkinian–come to stop Future Link from continuing being dictator. Future Link doesn't take this lightly, and kidnaps Younger Link. Then Future Link shoots the other three heroes. Link decides to commit suicide, the only way to save the future. Older Link dies, but younger Link survives. This glitch in time allows Evil Link to come into existence in the past, but leaves Evil Link dead in the present of 2040.

Civil war between Evil Link's minions ensues after Link's death. Link's empress, Pinkie Pie, assumes power at first, only for an elderly Mario to overthrow her with an army of Gay Luigi clones. Birdo, however, convinces the Gay Luigis to join her instead, and ultimately becomes the new military leader of Hyrule. Many Hylians disapprove of Birdo due to her disputed gender, but further civil war is averted when Birdo decides to share power with her husband, Yoshi.

Following Evil Link's death, a rebellion begins in many of the foreign territories occupied by Hyrule.